Jit
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PG2: Making Pangenome Graphs Easier to Understand
By Jitendra Narayan 47 days agoGenomics is moving beyond the traditional approach of studying DNA using a single reference genome. Today, researchers are increasingly using pangenomes, which represent genetic information from multiple genomes and capture a much broader range of...The Atlas of Nine Billion Possibilities
By Jitendra Narayan 25 days agoThis question led to the AlphaGenome Atlas (https://deepmind.google.com/science/alphagenome/atlas?), a detailed map of nearly every possible single-letter change in the human genome. Instead of checking each change one by one, researchers can use...Finding the Hidden Switches: The Story of KiNext and Protein Kinases
By LEGE 10 days agoEvery newly sequenced genome contains thousands of proteins, but identifying what each protein does is a much harder task. Among these proteins are protein kinases, important molecular regulators that control processes such as cell growth,...Heatmapper: web-enabled heat mapping for all
By Jit 2925 days agowww2.heatmapper.ca - Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety...LAST
By Archana Malhotra 3861 days agohttp://last.cbrc.jp/ - LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with...Stampy
By Abhi 3788 days agowww.well.ox.ac.uk - Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2967 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....RNA Sequencing Helps Identify Functional Variants from GWAS
By Andaleeb 4698 days agoschizophreniaforum.org - For Alzheimer’s and other complex disorders, mining the genome for disease-associated variants is no longer the obstacle. The challenge nowadays is figuring out how the identified loci relate to disease. As reported last month in Nature and...Barrnap: Bacterial ribosomal RNA predictor
By Abhimanyu Singh 3432 days agogithub.com - Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output....Meta-Transcriptomics: Dynamic World of RNA in Diverse Environments
By Abhi 795 days agoMeta-transcriptomics combines high-throughput sequencing technologies with computational biology to profile the RNA content of a sample.
